rs1445946

Variant names:

• chr5-16727425-C-T
• rs1445946
• NM_012334.3:c.1930-16180G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012334.3(MYO10):​c.1930-16180G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,072 control chromosomes in the GnomAD database, including 12,815 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (12815 hom., cov: 32)
• Consequence: MYO10 NM_012334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 1 publications found

Genes affected

MYO10 (HGNC:7593): (myosin X) This gene encodes a member of the myosin superfamily. The protein represents an unconventional myosin; it should not be confused with the conventional non-muscle myosin-10 (MYH10). Unconventional myosins contain the basic domains of conventional myosins and are further distinguished from class members by their tail domains. This gene functions as an actin-based molecular motor and plays a role in integration of F-actin and microtubule cytoskeletons during meiosis. [provided by RefSeq, Dec 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO10	NM_012334.3	c.1930-16180G>A		intron_variant	Intron 19 of 40	ENST00000513610.6	NP_036466.2
MYO10	XM_006714475.4	c.1861-16180G>A		intron_variant	Intron 18 of 39		XP_006714538.1
MYO10	XM_005248307.3	c.-1+14379G>A		intron_variant	Intron 1 of 22		XP_005248364.1
MYO10	XM_011514046.3	c.-1+10711G>A		intron_variant	Intron 1 of 22		XP_011512348.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO10	ENST00000513610.6	c.1930-16180G>A		intron_variant	Intron 19 of 40	1	NM_012334.3	ENSP00000421280.1

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54071 AN: 151954 Hom.: 12771 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.318

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.356 AC: 54183 AN: 152072 Hom.: 12815 Cov.: 32 AF XY: 0.349 AC XY: 25971 AN XY: 74362

African (AFR) AF: 0.674 AC: 27924 AN: 41460

American (AMR) AF: 0.352 AC: 5370 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 841 AN: 3468

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5176

South Asian (SAS) AF: 0.269 AC: 1298 AN: 4824

European-Finnish (FIN) AF: 0.167 AC: 1767 AN: 10574

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14679 AN: 67976

Other (OTH) AF: 0.316 AC: 668 AN: 2114

Alfa AF: 0.247 Hom.: 5073

Bravo AF: 0.385

Asia WGS AF: 0.273 AC: 947 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.21
DANN	Benign	0.26
PhyloP100		-0.71
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1445946; hg19: chr5-16727534;